Not all structures in the park are available for park use. An important structure that is available is the partially restored Fort Warren, an impressive granite Third System fortification designated as a National Historic Landmark, which has stood on Georges Island as a major defensive post for the protection of the harbor in every conflict from the Civil War through World War II. Fort Andrews, erected on Peddocks Island in the first decade of this century, is a rare example of a relatively intact coastal fort of the Endicott Period (1888-1905), although its 26 remaining buildings and structures have suffered over 50 years of abandonment and are generally in poor condition.
Navigational aids constructed to guide ships through the often treacherous harbor waters include Boston Light on Little Brewster Island, a National Historic Landmark purported to include portions of the oldest lighthouse structure in the United States; and two lights on the National Register of Historic Places, Graves Light on The Graves and Long Island Head Light on Long Island. Nixes Mate is a pyramidal channel marker that has stood in the harbor since the early 1900s.
Approximately 30 cottages on Peddocks Island, dating from the early 20th century, are the last remaining residential structures on the harbor islands (aside from year-round institutional residences on Thompson). They are occupied by their owners during the summer and allude to the former prevalence of summer communities and recreational activities in the harbor, as well as fishing communities. In recent years, the Massachusetts Department of Conservation and Recreation (DCR) has been acquiring, evaluating, and removing the cottages as owners vacate them.
On Deer Island an 1889 pump station, renovated for use as a visitor center, contains a community room and exhibits of historic pumps, recalling early attempts to deal concertedly and scientifically with the region's waste water that has been discharged into Boston Harbor since 1878. Contemporary structures include 12 egg-shaped sewage "digesters" each standing 170 feet high on the southern end of the island.